There’s a quite minimalistic but fully working (on Win7, too) exe on corkami/wiki/PE101, every byte of it is explained in the nice graphic. You can type it all by hand in a hex editor, but the paddings may make that a little tedious.
As for the history, yes someone at Microsoft invented the exe format (the old DOS MZ exe format) and he (or someone else at Microsoft) wrote a loader for it and a linker, which is the thing that traditionally turns the output of a compiler (“object files”) into executable files. It’s possible (and even likely, I would say) that the first exe programs were written by hand, after all they were only meant to test the new loader.
Later, AT&T’s COFF format was extended by Microsoft to the PE format, which still has the MZ header and typically (but optionally, it’s not in the corkami example, and it can be anything really) includes a small DOS program just to print the message “This program cannot be run in DOS mode”.